Abstract
Most commonly microorganisms are known as disease causing agents amongst common people but when we turn towards their positive aspects they do wonderful things. Microbes have remained an integral part of soil since ever earth originated. They are capable of turning soil into waste land and further into productive soil. A teaspoon of soil contains millions of bacteria which functions to increase soil fertility and plant growth by providing air, minerals and organic compounds. These microbes are primary decomposers of organic matter. The physical and chemical composition of soil varies throughout the earth. The soil bearing high number of microorganisms considered as most fertile soil. These tiny creatures ensure the permanent existence of nutrients in soil. Due to their role in pedogenesis and improvement of soil fertility these minute entities have become major subject of investigation in recent past. Nutrient development in soil is carried out via biological transformation through action of microorganism. Without microbes, soil would be a virtually inert (lifeless) body but with them, soil is truly a living, dynamic system. Microbes and the humus produced by them work as a glue to hold soil particles together in aggregates hence improves soil tilth and decrease soil depletion or erosion. Well aggregated soil provides the rightful combination of air and water to plant roots.
1 Introduction
Soil can be defined as the solid material on the surface of Earth resulting from the interaction of weathering and biological activity on the parent material or underlying hard rock. Pedogenesis (Greek term where pedo means ‘soil’ and genesis, means ‘origin) is the process of soil formation which is under regulation of effects of place, environment and history. Pedogenesis is a branch of pedology that is study of soil in its natural environment. Soil synthesis is a result of biogeochemical processes taking place within the soil. Such activities result in development of layers called soil horizons, differentiated by colour, texture, structure and chemistry (Buol et al. 1973). Pedogenesis basically involves physical, chemical and microbial weathering of rocks out of which physical and chemical processes are well studied. To our knowledge, microbial weathering is functionally and taxonomically least investigated. Till date, only lichens (symbiotic associations between fungi and photosynthetic algae or cyanobacteria) have been regarded as the first mineral weathering pioneer organisms (Banfield et al. 1999). Lichens colonized the same mineral spot on the surface of a rock or monument for decades and carried out its weathering. Interestingly, in lichens, complex microbial communities have been identified, such as bacteria belonging to Anabaena, Bradyrhizobium, Burkholderia and Collimonas (Gorbushina 2007; Seneviratne and Indrasena 2006). An indirect effect of Bradyrhizobium elkanii on the mineral-weathering ability of lichen has been reported (Seneviratne and Indrasena 2006): rather than directly weathering the mineral substrate the bacterium, fixes and supplies nitrogen to the fungus, enhancing fungal organic acid production. Howbeit, the relative impact of these types of bacteria on the weathering process is poorly understood.
1.1 Factors Involved in Soil-Formation
The soil-formation process include two active factors, climate and organisms, which carry out catalysis in pedogenesis and three passive factors (parent material, topography, and time) that respond to the forces exerted by active factors (Fig. 10.1).
1.2 Passive Soil Forming Factors
The passive soil forming factors are those which represent the source of soil forming mass and conditions affecting it. These provide a base on which the active soil forming factors work or act for the development of soil.
Parent material is that consolidated matter from which the soil is formed.
Climatic factors, temperature and rainfall directly affect soil. Weathering of rocks occurs quickly in warm and moist climates where temperature affects the rate of chemical as well as biological activity (Huddleston 1984). As far as organisms are concerned they exist mainly in two significant groups:
1. Macroorganisms
2. Microorganisms
2 Macroorganisms
Macroorganisms include living or dead large plants and animals. Dead and decaying plant matter build up organic matter in the soil. Live macroorganisms are the source of nearly all organic matter. Plants in the form of grasses, woody vegetation and trees contribute largely towards organic matter production. The positive effect of organic matter in the soil cannot be overemphasized (Thompson and Troeh 1973).
3 Microorganisms
Microorganisms or microbes are tiny entities that are not visible with naked eyes but only seen through microscope. Microbes play an important role in pedogenesis process where existing soil, rocks, water, air and organisms interact with each other (Bin et al. 2010). There exists a wide knowledge gap in the biological weathering of rocks, especially through microbes which is sparsely studied. Therefore in this chapter we have emphasized on the role of microbes mainly bacteria in pedogenesis. Bacteria are tiny, single-celled organisms – generally 4/100,000 of an inch wide (1 μm) and somewhat longer in length. What bacteria lack in size, they make up in numbers. In a teaspoon of productive soil bacteria ranges between 100 million and 1 billion in number which equals to mass of two cows per acre (Ingham 2009).
Bacteria, fungi, protozoa, nematodes, and algae are the primary decomposers of organic matter (Khatoon et al. 2017). They convert raw plant and animal residues into a complex, dark brown or black substance called humus, improve soil tilth and release soil nitrogen as an essential nutrient for plants Mosier et al. (2004). Microbes and the humus they produce, makes topsoil rich and fertile by acting as a glue to hold soil particles together in form of aggregates thus minimise soil erosion Coleman. Well-aggregated soil ideally provides the rightful combination of air and water to plant roots.
3.1 Mechanisms Involved in Pedogenesis By Bacteria
The soil is where living organisms, or the biosphere, interact with rocks and minerals (geosphere), water (hydrosphere), atmosphere and dead organic matter (detritosphere).
Without microbes, soil would be a virtually inert (lifeless) body. With them, soil is truly a living, dynamic system
The first assumption about bacteria playing major role in soil fertility and decomposition was typified by the book of Löhnis and Fred (1923). The nitrogen fixing Rhizobium, Mesorhizobium and Bradyrhizobium along with methanogens (Methylobacter and Methylophilus) have been implicated in weathering of minerals. Chitinase producing Collimonas may degrade live hyphae (de Boer et al. 2004) alone but along with Burkholderia they weather minerals aswell (Uroz et al. 2007). Nitrospira and Nitrobacter are the ammonia oxidisers, Thiobacillus- the iron oxidiser and Methylomonas is the methanotroph (Aislabie and Deslippe 2013).
3.2 Bacterial Weathering of Minerals:
Bare rock surfaces being in contact with air, could be a special habitat to microbes, even though they are featured by enormous fluctuating harsh environments including solar radiation, drought, nutrient deficiency and temperature, still various types of microorganisms exist in the cracks as well as on the rock surfaces (Gorbushina, 2007). Earlier some kinds of autotrophic photosynthetic nitrogen-fixers such as algae, cyanobacteria and lichens were described as rock microorganisms but later, some heterotrophic bacteria and fungi were also observed on exposed rocks surface. Although the rock surface is unsuitable for microbial survival, autotrophic microorganisms cope up with adverse conditions via photosynthesis and N fixation, whereas heterotrophic bacteria interact symbiotically with autotrophs (e.g. lichen type fungi) or intercept smaller soil particles to thrive nutrients which were occasionally brought in by air and rainwater (Viles and Gorbushina, 2003). These rocky microorganisms are of collaborative or symbiotic type, and differ from soil microbes that usually exist in competitive or predatory type of relationship thus are pioneers of species responsible for weathering of rocks (Burford et al. 2006; Gorbushina et al. 2003). Some bacteria, fungi, lichens and algae were identified or isolated from the surface of Triassic limestone and dolomite in Guizhou, Southwest China (Fig. 10.2) (Lian et al. 2008). Different microbes mainly work on retainment of water and trace nutrients for sustaining life activities and reproduction (Gorbushina, 2007). Under nutrient deficiency these microrganisms bore into the rock resulting in to small cave or tunnel, strengthening the colonization on the rock surface to form biofilm or biological crust under suitable conditions (such as favourable temperature and humidity) (Lian et al. 2008). Prokaryotic microorganisms usually have spores and exopolysaccharides to protect cells against desiccating conditions on the rock surface.
Recent research shows that in order to acquire energy, bacteria may be directly responsible for driving cascade of reactions that reduce rocks to soil and free biologically important minerals (Shelobolina et al. 2012). It has been reported that number of bacterial strains belonging to diverse genera (Pseudomonas, Streptomyces, Staphylococcus, Frateuria, Rhanella, Sphingomonas, Aminobacter, Burkholderia, Enterobacter, Agrobacterium, Achromobacter, Collimonas, Acinetobacter, Azotobacter, Citrobacter, Shewanella, Serratia, Bacillus, Mycobacterium, Arthrobacter and Rhizobium) are capable of mineral-weathering (Uroz et al. 2009). Such bacteria are able to effect mineral stability alone or in combination with other microorganisms by making complex microbial communities that colonize mineral surfaces. Albeit most of the functional studies reported have emphasized on bacterial isolates from soil. Stones act as primary ecosystems due to their exclusive mineral composition where only a few adapted microbes possessing mineral-weathering abilities, can grow and survive (Calvaruso et al. 2007; Uroz et al. 2007).
Bacterial weathering of minerals in soil has remained the target of most functional studies concerned with bacterial abilities for mineral weathering. These rock surfaces are complex environments and diversified in composition that are usually colonized by specific bacteria (Fig. 10.3) that vary from those inhabiting the surrounding soil (Uroz et al. 2009). Furthermore, the surface and the core of soil mineral particles seems to be inhabited by non similar bacterial communities: in limestone, the endolithic bacterial community seemed to be composed mainly of Gram-positive bacteria and acidobacteria, whereas the epilithic population was composed of approximately 50% proteobacteria (McNamara et al. 2006). Mineral particles contain inorganic nutrients (aluminium, silica and calcium) which are used by these bacteria thus mineral composition is another key factor influencing bacterial communities. Bacteria have been reported by Gleeson et al. (2006) and Carson et al. (2007) for colonization of different primary minerals such as granite, limestone, apatite, plagioclase, quartz, however, the fingerprints of bacterial communities colonizing granite varied with mineral inclusion (muscovite, plagioclase, Kfeldspar and quartz). All these observations showing correlation between mineral composition and bacterial communities prompts us to propose a new concept, the mineralosphere.
3.3 Rhizosphere and Mineralosphere
It is well established that, in the rhizosphere, only 1–2% of bacteria promote plant growth and act as biofertilizers (Antoun and Kloepper 2001). The rhizosphere effect is well known from the beginning of the twentieth century (Hiltner 1904). The proliferation of soil microorganisms in the vicinity of plant roots get influenced via root exudation which are preffered food source for microbes (Walker et al. 2003). The rhizosphere is a hot-spot of plant microbe interactions leading to efficient geochemical cycling of nutrients. Rhizospheric region of the soil is rich in primary and secondary metabolites that orchestrate almost every type of rhizospheric interaction where plant roots communicate with their below-ground microbial residents. A biochemical signal is conducted between rhizobacteria and plant roots resulting in dynamic interactions flourishing either symbiosis or pathogenicity (Vessey and Buss 2002). Rhizosphere contains innumerable secondary metabolites where particularly flavonoids and auxins are documented to be the most important signalling elements in plant-microbe interactions. Numerous rhizobacterial species which are known to facilitate plant growth by exerting beneficial effects are generally referred to as plant growth promoting rhizobacteria (PGPR) (Vera et al. 2013). These are most widely studied beneficial, saprophytic, heterogenous group of rhizospheric bacteria which aids in the plant growth through direct and indirect mechanisms via nitrogen fixation, solubilization of zinc and phosphorus, lowering of ethylene concentration through ACC-deaminase activity under abiotic and biotic stressed conditions, production of plant hormones such as indole acetic acid (IAA), gibberellins and cytokinins, production of siderophores and competitive exclusion of pathogens or elimination of substances toxic to plants (Prasad et al. 2017).
The surroundings of soil minerals, where microorganisms are selected for their ability to preferentially use the inorganic nutrients released by soil minerals, such mineral-influenced habitats are called as ‘mineralosphere’. In accordance to Uroz et al. (2007) the ‘mineralosphere’ signifies the specific interface and habitat comprising the rock surfaces and the surrounding soil, which are physically, chemically and biologically influenced by minerals. Physically, the mineralosphere is characterized by several zones, including pores and cracks which modify water circulation and can be considered as microbial sanctuaries. Bacteria get accumulated in such mineralospheric zones via passive diffusion, and develop relative protection against external environmental stresses (abiotic and biotic). Chemically, it is a nutrient reserve and an active interface where surface charges and the minerals exchange capacity exhibit impact on colonization of mineral surfaces. Indeed, positive charges (such as in the phyllo silicate inter layers) can attract negatively charged bacterial cells (Uroz et al. 2007). Due to nutritional value or toxicity of nutrients contained within minerals they can attract or repel microbes. Released nutrients have direct availability to bacteria, but in case of unavailable nutrients microbes can carry out precipitatation (oxides) through solubilization to make them available (Uroz et al. 2009). Biologically, this habitat is enriched in low-carbon and mineral-rich environments adapted microorganisms which potentially contribute towards mineral weathering. In mineralosphere, the mineral-weathering capability of bacteria may be regulated by their nutritional requirements, nutrient availability, and/or the mineral type. Undoubtedly, this habitat is under great influence of environmental factors, including soil parameters such as pH and water availability, or the organic and inorganic nutrient inputs. Generally, the carbonate rocks are enriched in Ca, Mg and lack of Si, Al, and Fe, but soil inorganic substances are mainly Si, Al, Ca, Mg, Fe, etc. Rocks cannot be weathered easily to supply a large number of soil minerals. The microorganisms in such areas erode the rocks by forming micro-colonies, biofilms, and biological crust on the rock surface or in micro-cracks through the chemical degradation (organic acids secreted by the microbial metabolism to promote calcium carbonate dissolution and weathering), the biological effect (the mineral particles are broken down via microbial growth along with interspersed fungal hyphae to erode rock surface more easily) and the enhancement of erosion via bacterial metabolites or enzymes (microorganisms secrete enzymes such as carbonic anhydrase enzymes etc.) to speed up the weathering of calcium carbonate (Dou and Lian 2009; Chen et al. 2008). Lepleux et al. (2012) performed a BIOLOG analysis to highlight potent mineral-weathering bacterial isolates in contrast to those of the surrounding bulk soil or the mycorrhizo-sphere, where mineral-associated (mineralosphere) bacteria exhibited oligotrophic behaviour by metabolizing only few substrates and that too with a very low intensity. Interestingly, the most intensively and unique substrate utilized by the mineralospheric bacteria appeared to be glucose. On the other hand, bacteria from the bulk soil prefer to metabolize amino and carboxylic acids with high intensity, with comparatively poor glucose metabolism. It has been reported that the most efficient mineral-weathering bacteria produce high concentrations of oxalate (Frey et al. 2010). These observations demonstrate that mineral-associated bacterial isolates are physiologically active, metabolize organic substrates, and produce metabolites, suggesting that they may participate in mineral weathering and nutrient cycling and finally in pedogensis.
Rhizosphere and mineralosphere both are important zones of biotic interactions and both provide physical support to life (Fig. 10.4). Due to some common traits such as nutrient bioavailability and uptake (Nitrogen fixation, P, S, K and Zn solubilisation by rhizospheric bacteria and inorganic mineral nutrients Ca, Mg, K, Na, Al, Fe, Mn by mineralospheric bacteria through production of organic acids and metal chelators along with siderophores production for iron acquisition), biofilm production, antagonism and decomposition of organic compounds and mineral precipitation. All these factors suggest that mineralopshere is the inorganic twin to rhizosphere (Uroz et al. 2009).
4 Minerals Regulating Bacterial Gene Expression
From above studies it is apparent that bacterial communities colonize minerals, but this question also prompts in our mind that is there any effect of these minerals on the physiology of the bacteria under the influence of mineralosphere. To answer this question many attempts have been made using chemoheterotrophic bacteria able to respire in metals contained within minerals. Expression of different genes and protein production was observed when the bacterial cells formed biofilms on minerals (Vera et al. 2013). To address the above question Olsson-Francis et al. (2010) used a microarray approach to decrypt the molecular mechanisms by using Cupriavidus metallidurans CH34 to weather basalt in a minimal medium lacking iron. Their microarray analyses revealed that only in the absence of basalt siderophores were produced and other functional genes were up- or down regulated. It was noticed that when basalt was present in the minimal medium, multiple genes involved in transport and motility were upregulated whereas genes encoding TonB-dependent outer membrane transporter and ostensive cytochromes were downregulated. In similar context, Almario et al. (2013) reported that during interaction of Gaeumannomyces graminis–Pseudomonas, production of 2,4-diacetylphloroglucinol was induced significantly higher in the presence of iron-rich vermiculite than in the presence of illite when they were trying to decipher the effect of iron availability on the 2,4-diacetylphloroglucinol production by Pseudomonas CHA0. Hence, these above mentioned results suggest that, physico- chemical properties of minerals, influence gene expression of bacteria residing in mineralosphere.
5 Bacteria and Nutrient Cycling
Soils constitute highly complex ecosystems where different biogeochemical cycles interact with each other such as carbon, nitrogen, phosphorus and sulphur. And, microbes add to soil’s complexity by mediating most of these biogeochemical interactions. Soil is the site for organic matter decomposition and nutrient mobilisation via oxidation and reduction reactions of nutrient elements, symbiotic N-fixation and photoautotrophic activity. These activities of soil are carried out by bacteria, archaea and fungi which together drive nutrient cycling and weathering of minerals. In soils, microbes play a pivotal role in nutrient cycling through processes like decomposition and mineralisation. Soil microbes carry out decomposition by degrading nonliving organic matter to get energy for growth. Mineralisation takes place when organic components get completely degraded into inorganic products such as carbon dioxide, ammonia, and water.
5.1 Bacteria and Soil Nitrogen
Among the autotrophs are nitrite oxidisers in the genera Nitrospira and Nitrobacter, and phototrophs in Rhodospirillum and Rhodobacter. Members of Burkholderia are also reported to fix nitrogen and promote plant growth (Aislabie and Deslippe 2013).
5.2 Bacteria and Soil Carbon
When we stand on soil, we are standing on an important reservoir of the carbon cycle from where large amount of carbon is added to the atmosphere. Microbes play major roles in the cycling of carbon- the key constituent of all living organisms. In terrestrial ecosystems, CO2 gets fixed in to organic matter by primary producers (plants, algae and cyanobacteria). Within soil, autotrophic microbes can also fix carbon dioxide. Heterotrophic bacteria and fungi degrade complex organic molecules that higher organisms cannot do hence they are the ultimate recyclers of non-living organic matter. Numerous Actino and Proteobacteria, degrade soluble organic acids, amino acids, and sugars (Eilers et al. 2010). Some bacteria, such as Bacteroidetes target recalcitrant carbon compounds (cellulose, lignin and chitin) and they perform well in N rich environments in order to support the production of extracellular and transport enzymes (Treseder et al. 2011). In contrast, bacteria adapted to low levels of N are more likely to metabolise nitrogenous organic compounds such as amino acids. It has been reported that overall mineralisation of soil’s carbon is positively correlated with abundance of β-Proteobacteria and Bacteroidetes but exhibit negative correlation with Acidobacteria (Fierer et al. 2007). Fermentative microbes can anaerobically degrade organic compounds in to organic acids resulting in generation of gases such as H2 and CO2. Further under strict anaerobic environment the hydrogen may be utilized by methanogens to reduce CO2 in to methane CH4 gas. Some methanogens can metabolise methanol, acetate or methylamine to methane and carbon dioxide.
6 Bacteria and Soil Bioremediation
Absorption, detoxification and recycling of applied wastes (e.g. effluent disposal), agrochemicals and oil spills takes place in soil attributed to its microbial activities which makes soil healthy and reduces potential harm to humans and ecosystem. Microbial processes like mineralisation and immobilisation are responsible for these services. This detoxification of soil through microbial intervention is known as soil bioremediation. Detoxifying microbes may be limited by the availability of soil nutrients (e.g. N or P), which in turn depends on soil microbial activities. The heterotrophic bacteria Sphingomonas are known to degrade a range of toxic compounds (pentachlorophenol and polyaromatic hydrocarbons) (Aislabie and Deslippe 2013). More oftenly implicated bacterial genera reported for oil degradation belong to spp. Pseudomonas, Sphingomonas and Mycobacterium. Amongst all Pseudomonas have been studied well for utilizing alkanes, monoaromatics, naphthalene, and phenanthrene as a sole carbon source under aerobic conditions via degradation through enzymes (Kuran et al. 2014). The mechanisms being employed by these oil degrading bacteria have been applied in situ. For example, enhancing oil degradation in soil typically involves addition of nutrients (N and P) and sometimes oxygen and water. Due to ubiquitous nature of hydrocarbon-degrading bacteria there is no need to add them to oil-contaminated sites in soil besides they increase in number when oil is spilled. Howbeit, elevated hydrocarbon concentration leads to depletion of available N and P due to their assimilation during biodegradation; consequently, activity of the hydrocarbon degraders may become limited by these nutrients (Lang et al. 2016).
Bacteria and fungi also degrade pesticides. Example of the bacteria degrading pesticide is Arthrobacter nicotinovorans HIM that utilized atrazine as a sole source of C and N and also degraded the related triazine compounds simazine, terbuylazine, propazine, and cyanazine (Aislabie et al. 2005). Biodegraded pesticides in soil are usually ineffective to control pests. Pesticides like DDT are not readily degradable so persist in soil and when aerobic conditions are available DDT is converted to DDE, which has been regarded as a dead-end metabolite. Terrabacter sp. Strain DDE-1, metabolised DDE when grown on biphenyl (Aislabie et al. 1999). Leaching of pollutants like excess of nutrients, heavy metals and organic compounds into soils is another environmental issue which can contaminate ground water and aquatic ecosystems which are life threatening events for humans. Soils absorb and retain solutes and pollutants, avoiding their release into water. Microbial products contribute to soil’s hydrophobicity and wettability, both that impacts on the soils ability to filter contaminants (Aislabie et al. 2005).
7 Future Prospective
Based on recent studies presented above a new concept the ‘mineralosphere’ has came in to the picture which forms the basis of pedogenesis through action of microbes mainly bacteria. Exact mechanisms and their survival tendency in mineralosphere is yet to be investigated thoroughly so it is perquisite to implement recent molecular techniques to study diversity analysis and to unravel 99% undiscovered microbiota from the environment. These tiny creatures ensure the permanent existence of nutrients in soil. Due to their role in pedogenesis and improvement of soil fertility these minute entities have become major subject of investigation in recent past. Further research is desired for comparison of mineral-weathering potentials of bacterial isolates from the mineralosphere to those of rhizospheric bacteria to characterize this unexplored niche.
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Sharma, P., Bhakri, G. (2019). Role of Bacteria in Pedogenesis. In: Varma, A., Choudhary, D. (eds) Mycorrhizosphere and Pedogenesis. Springer, Singapore. https://doi.org/10.1007/978-981-13-6480-8_10
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